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Sci Rep. 2018 Aug 9;8(1):11904. doi: 10.1038/s41598-018-30383-z.

A single N1-methyladenosine on the large ribosomal subunit rRNA impacts locally its structure and the translation of key metabolic enzymes.

Author information

1
Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, D-60438, Germany. ssharma33@mgh.harvard.edu.
2
RNA Molecular Biology, Fonds National de la Recherche (F.R.S./FNRS), ULB-Cancer Research Center (U-CRC), Center for Microscopy and Molecular Imaging (CMMI), Université Libre de Bruxelles (ULB), BioPark campus, B-6041, Gosselies-Charleroi, Belgium. ssharma33@mgh.harvard.edu.
3
Massachusetts General Hospital Centre for Cancer Research and Department of Medicine, Harvard Medical School, Boston, 02129, USA. ssharma33@mgh.harvard.edu.
4
Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, D-60438, Germany.
5
RNA Molecular Biology, Fonds National de la Recherche (F.R.S./FNRS), ULB-Cancer Research Center (U-CRC), Center for Microscopy and Molecular Imaging (CMMI), Université Libre de Bruxelles (ULB), BioPark campus, B-6041, Gosselies-Charleroi, Belgium.
6
Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, D-60438, Germany. entian@bio.uni-frankfurt.de.

Abstract

The entire chemical modification repertoire of yeast ribosomal RNAs and the enzymes responsible for it have recently been identified. Nonetheless, in most cases the precise roles played by these chemical modifications in ribosome structure, function and regulation remain totally unclear. Previously, we demonstrated that yeast Rrp8 methylates m1A645 of 25S rRNA in yeast. Here, using mung bean nuclease protection assays in combination with quantitative RP-HPLC and primer extension, we report that 25S/28S rRNA of S. pombe, C. albicans and humans also contain a single m1A methylation in the helix 25.1. We characterized nucleomethylin (NML) as a human homolog of yeast Rrp8 and demonstrate that NML catalyzes the m1A1322 methylation of 28S rRNA in humans. Our in vivo structural probing of 25S rRNA, using both DMS and SHAPE, revealed that the loss of the Rrp8-catalyzed m1A modification alters the conformation of domain I of yeast 25S rRNA causing translation initiation defects detectable as halfmers formation, likely because of incompetent loading of 60S on the 43S-preinitiation complex. Quantitative proteomic analysis of the yeast Δrrp8 mutant strain using 2D-DIGE, revealed that loss of m1A645 impacts production of specific set of proteins involved in carbohydrate metabolism, translation and ribosome synthesis. In mouse, NML has been characterized as a metabolic disease-associated gene linked to obesity. Our findings in yeast also point to a role of Rrp8 in primary metabolism. In conclusion, the m1A modification is crucial for maintaining an optimal 60S conformation, which in turn is important for regulating the production of key metabolic enzymes.

PMID:
30093689
PMCID:
PMC6085284
DOI:
10.1038/s41598-018-30383-z
[Indexed for MEDLINE]
Free PMC Article

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